When provided with both choices of pre-exposure prophylaxis (PrEP) in MSM, men may choose to use either method based on their sexual practice. The study objective was to describe the switches between dosing regimens and identify factors that predict choice of a dosing regimen among MSM. We performed a multi-center, observational, prospective PrEP cohort study conducted at three study sites in Taiwan between January 2018 and March 2019. A total of 215 participants made 469 visits. In half of the visits (49.7%), participants reported using on-demand PrEP. There were 36 regimen switches: 20 from daily to on-demand and 16 from on-demand to daily. Among 28 participants who switched regimens, 22 switched regimens once and 6 switched more than once. The frequency of condomless anal sex and a history of post-exposure prophylaxis use were associated with taking PrEP on-demand (p < 0.05). PrEP adherence intervention should be tailored specifically to sexual behavior to increase adherence to PrEP.